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lesson 4: link to mothur.pbs also broken #1

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bff9413
Initial commit
michberr May 25, 2016
61276cf
Updated Readme.md with link to gh-page
michberr May 25, 2016
b197958
Created lesson 01-getting-started
michberr May 28, 2016
5bf7284
1) Added lesson 02-login: decided to split up login
michberr May 28, 2016
ae280c9
Merge branch 'gh-pages' of github.com:DenefLab/flux-tools into gh-pages
michberr May 28, 2016
9a3f4c8
Updates to lesson 01-getting-started
michberr May 29, 2016
a957554
Fixed numbering on index.md
michberr May 29, 2016
9539606
Updates to lesson 02-login
michberr May 29, 2016
c242b20
Created lesson 03-jobs
michberr May 31, 2016
8ae6b5e
Created lesson 04-mothur and added mothur ex scripts
michberr May 31, 2016
41f8213
Added navigation section to lesson 02
michberr May 31, 2016
a71f4a4
Updates to index.md
michberr May 31, 2016
2587539
Created lesson 05
michberr Jun 1, 2016
42b3ee6
Clarified role of different drives in lesson 02
michberr Jun 1, 2016
8a10e39
Fixed mothur.pbs
michberr Jun 1, 2016
1abe650
fixed link in lesson 4 to mothur.batch
michberr Jul 8, 2016
6a5d1ba
Changed lesson 2 to duo authentication instead of mtoken
michberr Aug 23, 2016
20cb924
Updated Readme.md
michberr Aug 23, 2016
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7 changes: 6 additions & 1 deletion README.md
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# flux-tools
Code and demos for running scripts on FLUX
This is a repo containing demos for how to get started with the University of Michigan FLUX HPC cluster and run some basic bioinformatics/microbiome scripts.

You can access lessons at [http://deneflab.github.io/flux-tools/](http://deneflab.github.io/flux-tools/).

This repo was created by @michberr. As of September 2016 updates to flux may not be reflected in the demos.

12 changes: 12 additions & 0 deletions _includes/header.html
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<link rel="shortcut icon" type="image/x-icon" href="{{page.root}}/favicon.ico" />
<link href="{{page.root}}/css/bootstrap/bootstrap.css" rel="stylesheet" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link href="{{page.root}}/css/bootstrap/bootstrap-responsive.css" rel="stylesheet" />
<link rel="stylesheet" type="text/css" href="{{page.root}}/css/swc.css" />
<link rel="stylesheet" type="text/css" href="{{page.root}}/css/swc-bootstrap.css" />
<meta charset="UTF-8" />
<meta http-equiv="last-modified" content="{{site.timestamp}}" />
<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
<!--[if lt IE 9]>
<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
5 changes: 5 additions & 0 deletions _includes/javascript.html
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<!-- Le javascript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="{{page.root}}/js/jquery-1.9.1.min.js"></script>
<script src="{{page.root}}/js/bootstrap/bootstrap.min.js"></script>
29 changes: 29 additions & 0 deletions _layouts/lesson.html
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---
---
<!DOCTYPE html>
<html>
<head>
{% if page.title %}
<title>{{ page.title }}</title>
{% endif %}
{% include header.html %}
<link rel="stylesheet" type="text/css" href="{{page.root}}/css/lesson.css" />
</head>
<body>
<div class="container">

<div class="row-fluid">
<div class="span10 offset1">
<!-- start content -->
{% if page.title %}
<h1>{{page.title}}</h1>
{% endif %}
{{content}}
<!-- end content -->
</div>
</div>

</div>
{% include javascript.html %}
</body>
</html>
60 changes: 60 additions & 0 deletions _layouts/slides.html
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---
cdn: http://files.software-carpentry.org/cdn
---
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<title>{{page.title}}</title>
<meta name="description" content="{{page.title}}" />
<meta name="author" content="{{page.author}}" />
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no" />
<link rel="stylesheet" href="{{page.cdn}}/reveal.js/css/reveal.min.css" />
<link rel="stylesheet" href="{{page.cdn}}/reveal.js/css/theme/default.css" id="theme" />
<!--[if lt IE 9]>
<script src="lib/js/html5shiv.js"></script>
<![endif]-->
<link rel="stylesheet" href="{{page.cdn}}/bootstrap/bootstrap.css" />
</head>
<body>

<div class="reveal">
<div class="slides">
{{content}}
</div>
</div>

<script src="{{page.cdn}}/reveal.js/lib/js/head.min.js"></script>
<script src="{{page.cdn}}/reveal.js/js/reveal.min.js"></script>

<script>
// Full list of configuration options available at http://github.com/hakimel/reveal.js#configuration.
Reveal.initialize({
controls: true,
progress: true,
history: true,
center: true,

theme: 'sky',
transition: 'none',

// Parallax scrolling
// parallaxBackgroundImage: 'https://s3.amazonaws.com/hakim-static/reveal-js/reveal-parallax-1.jpg',
// parallaxBackgroundSize: '2100px 900px',

// Optional libraries used to extend on reveal.js
dependencies: [
{ src: '{{page.cdn}}/reveal.js/lib/js/classList.js', condition: function() { return !document.body.classList; } },
{ src: '{{page.cdn}}/reveal.js/plugin/markdown/marked.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } },
{ src: '{{page.cdn}}/reveal.js/plugin/markdown/markdown.js', condition: function() { return !!document.querySelector( '[data-markdown]' ); } },
{ src: '{{page.cdn}}/reveal.js/plugin/highlight/highlight.js', async: true, callback: function() { hljs.initHighlightingOnLoad(); } },
{ src: '{{page.cdn}}/reveal.js/plugin/zoom-js/zoom.js', async: true, condition: function() { return !!document.body.classList; } },
{ src: '{{page.cdn}}/reveal.js/plugin/notes/notes.js', async: true, condition: function() { return !!document.body.classList; } }
]
});
</script>

</body>
</html>
42 changes: 42 additions & 0 deletions _layouts/workshop.html
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---
---
<!DOCTYPE html>
<html>
<head>
{% if page.title %}
<title>{{ page.title }}</title>
{% else %}
<title>{{ page.venue }}</title>
{% endif %}
{% include header.html %}
<meta name="venue" content="{{page.venue}}" />
<meta name="date" content="{{page.humandate}}" />
<meta name="startdate" content="{{page.startdate}}" />
<meta name="enddate" content="{{page.enddate}}" />
</head>
<body>
<div class="container">
<div class="span10 offset1">
{% include banner.html %}

<div class="hero-unit">
<div class="row-fluid">
<div class="span10">
<h2>A Data Carpentry Workshop</h2>
<h4>Organized by ... </h4>
<h2>{{page.venue}}</h2>
{% if page.address %}{{page.address}}<br/>{% endif %}
{{page.humandate}}
{% if page.humantime %}<br/>{{page.humantime}}{% endif %}
</div>
</div>
</div>

{{content}}

{% include footer.html %}
</div>
</div>
{% include javascript.html %}
</body>
</html>
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